Genome-scaled phylogeny of Saccharomyces cerevisiae from spontaneous must fermentations

Modern winemakers commonly inoculate selected S. cerevisiae strains in must to obtain controlled fermentations and reproducible products. However, wine has been produced for thousands of years using spontaneous fermentations from wild strains, a practice that is experiencing a revival among small wine producers. Despite the widespread usage of such strains in the past, there is much to know about their ecology, evolution and functional potential. For example, the reciprocal affinities of these strains within the S. cerevisiae phylogeny have yet to be discovered, as well as the degree of their biodiversity and their impact on wine terroir. To fill this knowledge gap, we aim at characterising at strain level the S. cerevisiae present in spontaneously fermented musts sampled across Italy. We set up a protocol based on polyphenols-removing prewashes, followed by whole-genome shotgun sequencing at a depth of 5Gb of DNA per sample. We performed both an assembly-free analysis to reconstruct the strain-level phylogeny of S. cerevisiae strains using the species-specific-marker based StrainPhlAn, and the reconstruction of Metagenome-Assembled Genomes of these strains for downstream functional analyses. To plan conservation acts in a scenario of continuous climate change, we aim at isolating and maintaining strains of interest. We will present preliminary results from the analysis of spontaneous musts sampled at different fermenting stages

Shallow whole-genome sequencing of Aedes japonicus and Aedes koreicus from Italy and an updated picture of their evolution based on mitogenomics and barcoding

Aedes japonicus and Aedes koreicus are two invasive mosquitoes native to East Asia that are quickly establishing in temperate regions of Europe. Both species are vectors of arboviruses, but we currently lack a clear understanding of their evolution. Here, we present new short-read, shallow genome sequencing of A. japonicus and A. koreicus individuals from northern Italy, which we used for downstream phylogenetic and barcode analyses. We explored associated microbial DNA and found high occurrences of Delftia bacteria in both samples, but neither Asaia nor Wolbachia. We then assembled complete mitogenomes and used these data to infer divergence times estimating the split of A. japonicus from A. koreicus in the Oligocene, which was more recent than that previously reported using mitochondrial markers. We recover a younger age for most other nodes within Aedini and other Culicidae. COI barcoding and phylogenetic analyses indicate that A. japonicus yaeyamensis, A. japonicus amamiensis, and the two A. koreicus sampled from Europe should be considered as separate species within a monophyletic species complex. Our studies further clarify the evolution of A. japonicus and A. koreicus, and indicate the need to obtain whole-genome data from putative species in order to disentangle their complex patterns of evolution

Personalizing Cancer Pain Therapy: Insights from the Rational Use of Analgesics (RUA) Group

Introduction: A previous Delphi survey from the Rational Use of Analgesics (RUA) project involving Italian palliative care specialists revealed some discrepancies between current guidelines and clinical practice with a lack of consensus on items regarding the use of strong opioids in treating cancer pain. Those results represented the basis for a new Delphi study addressing a better approach to pain treatment in patients with cancer. Methods: The study consisted of a two-round multidisciplinary Delphi study. Specialists rated their agreement with a set of 17 statements using a 5-point Likert scale (0 = totally disagree and 4 = totally agree). Consensus on a statement was achieved if the median consensus score (MCS) (expressed as value at which at least 50% of participants agreed) was at least 4 and the interquartile range (IQR) was 3–4. Results: This survey included input from 186 palliative care specialists representing all Italian territory. Consensus was reached on seven statements. More than 70% of participants agreed with the use of low dose of strong opioids in moderate pain treatment and valued transdermal route as an effective option when the oral route is not available. There was strong consensus on the importance of knowing opioid pharmacokinetics for therapy personalization and on identifying immediate-release opioids as key for tailoring therapy to patients’ needs. Limited agreement was reached on items regarding breakthrough pain and the management of opioid-induced bowel dysfunction. Conclusion: These findings may assist clinicians in applying clinical evidence to routine care settings and call for a reappraisal of current pain treatment recommendations with the final aim of optimizing the clinical use of strong opioids in patients with cancer

Codon usage indicates that amphibians, reptiles and birds are major hosts for Zika and other arboviruses: implications for epidemiology and surveillance

Codon usage studies estimate the efficiency of viral replication in putative hosts and vectors for which there has been a supposed history of adaptation. This can help reconstructing the global epidemiology of arthropod-borne viruses (arboviruses), clarifying aspects regarding their ecology and evolution. Current studies concentrate on primate hosts, promoting a lack of information about alternative reservoirs. We studied if and how the codon usage of a set of 13 arboviruses comprising Zika, chikungunya, dengue, and yellow fever is adapted to a range of 30 different putative animal hosts. Our results indicate that all considered arboviruses are more adapted to amphibians, reptiles and birds than to humans and other mammals. This outcome is consistent over different indexes and correlates with the same analyses in West Nile and Japanese encephalitis viruses, two arboviruses known for their bird-to-bird transmission cycle. This is an unexpected finding indicating that non-mammals are the likely primary hosts of most arboviruses. Thus, we advocate that wild environments may have a stronger influence than previously thought in the reservoiring and spreading of Zika and other arboviruses. This has profound implications for the actual surveillance and management of outbreaks

On the correct interpretation of similarity index in codon usage studies: Comparison with four other metrics and implications for Zika and West Nile virus

Viruses can modify the usage of their synonymous codons to mimic that of their hosts: investigation of codon usage may therefore help increase our understanding of virus biology. The similarity index (SiD or (D(A,B)) is a recent method for estimating the resemblance of the overall codon usage of the hosts to that of a certain virus. Here we report that this index has been systematically misinterpreted in the literature. We first review its mathematical meaning to show that a high value of SiD indicates low codon usage similarity, and not the opposite as frequently reported. We further compared SiD with four other metrics - nCAI, nRCDI, ITE and tAI - using Zika and West Nile arboviruses in relation to various vectors and hosts. We highlight some differences between the five metrics and present a first bioinformatic evidence that Zika virus is poorly adapted to Culex quinquefasciatus, in accordance with the known biology of this virus. We conclude that SiD, if correctly interpreted, is a useful tool for codon studies, but we advocate that the results from this and other methods are context and time dependent and should be taken with car

Using codon usage bias to investigate the role of alternative vectors in the spread of Zika alternative

In the last years, outbreaks of Zika virus (ZIKV) and Dengue have been reported from both endemic and newly invaded areas areas of the world. ZIKV is in general associated with, and is well adapted to, primates and mosquitoes vectors, on which it can complete its cycle. Unfortunately, there is insufficient information regarding other animal reservoirs and amplification hosts, but there's a concrete possibility that ZIKV can infect other species, including domestic animals both from endemic and newly invaded temperate areas; such knowledge is fundamental to properly describe the epidemiology of ZIKV and plan its management. Unfortunately, large scalescreenings of putative alternative vectors, is extremely time and cost consuming. We suggest to employ Codon Usage Bias (CUB, (the adaptive similarity of codon usage ofvirus to that of its hosts), to predict if alternative hosts, in particular those associated with humans, can vehicle ZIKV. This will be performed by contrasting codon usage of ZIKVof hosts deduced from trascriptomes/proteomes, calculating parameters like RSCU (relative synonymous codon usage), CAI (codon adaptation index) and ENC (effective number of codons). Our first results indicate that Zika has putatively poor replication efficiency in Culex Pipiens. Ultimately, we advocate the analyses of CUB to understand evolutionary dynamics of ZIKV and other flaviviruses and better forecast their future outbreaks

Anemia and ischemia: Myocardial injury in patients with gastrointestinal bleeding

Acute gastrointestinal bleeding can produce hypovolemia, hypotension, and diminished oxygen-carrying capacity, causing myocardial ischemia and necrosis. Activation of the sympathetic nervous system can further increase myocardial oxygen demand and worsen ischemia. These processes would be expected to be most important in patients with obstructive coronary artery disease, a group that is also at risk for gastrointestinal bleeding.1,2 Studies examining the relationship between gastrointestinal bleeding and myocardial ischemia suggest that the prevalence of acute myocardial infarction in patients with gastrointestinal hemorrhage ranges from 1 to 14%.1-3 Cardiac troponins are highly specific and sensitive markers of myocardial injury.6-8 However, there has been no systematic study using troponin to define myocardial injury in patients with acute gastrointestinal bleeding and anemia. Prior studies that included patients with acute anemia and myocardial injury, defined by troponin elevation, were designed to evaluate patients hospitalized with any critical illness.9,10 Furthermore, there is no general agreement about risk stratification of myocardial injury in patients with acute upper gastrointestinal bleeding. There is some suggestion that those with a greater number of coronary risk factors, a history of coronary artery disease, a lower blood pressure on admission, older age, severe illnesses, and/or lower hemoglobin are at greater risk of myocardial infarction.1-5 The aim of the present study is to examine the relationship between hemoglobin and the risk of myocardial injury, defined as an elevation of troponin I, in patients with anemia secondary to upper gastrointestinal bleeding and no other clinical signs or symptoms of coronary insufficiency on enrollment. These findings and other possible predictors of myocardial injury were examined during the hospitalization